Hi, This is why you should actually copy and paste your command lines so you don't waste your time ;-) And mine.
Unless you wrote your entire system to your xtc file, your tpr has more atoms than your xtc, and thus probably some more dihedrals. Make a matching subset of your tpr using gmx convert-tpr, and use that with gmx rama -s. Mark On Wed, Jun 7, 2017 at 10:41 AM RAHUL SURESH <drrahulsur...@gmail.com> wrote: > Dear Mark > Thank you > > gmx rama -f traj.xtc -s topol.tpr -o ramachandran.xvg > > This was my command.. > > I didn't choose any dihedral particularly > > > On Wed, 7 Jun 2017 at 2:00 PM, Mark Abraham <mark.j.abra...@gmail.com> > wrote: > > > Hi, > > > > Sounds like your choice of dihedrals doesn't match your system. How did > you > > select them? > > > > Mark > > > > On Wed, 7 Jun 2017 08:41 RAHUL SURESH <drrahulsur...@gmail.com> wrote: > > > > > Dear Users > > > > > > When I try to execute ramachandran plot analysis, I get the following > > note > > > like "Dihedral around 5809,5816 not found in topology. Using mult=3" > > > (nearly 30-40 dihedrals). What is it about? > > > > > > Input is just protein structure extended upto 150ns. > > > > > > -- > > > *Regards,* > > > *Rahul Suresh* > > > *Research Scholar* > > > *Bharathiar University* > > > *Coimbatore* > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > *Regards,* > *Rahul Suresh* > *Research Scholar* > *Bharathiar University* > *Coimbatore* > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.